Emergent Mass and Coupling Ratios from Resonant Knot Solitons in R-Theory (Work Model) Methods + reproducibility upgrade

This record is the reproducibility-focused companion to the R-Theory work model on emergent mass and coupling ratios from resonant knot solitons. It is written as a practical “cookbook” for independently reproducing the numerical pipeline: how knot sectors are initialized and stabilized, how the topological charge Q is monitored (to prevent topology loss), and how convergence and failure modes are diagnosed. The document specifies recommended simulation choices (domain size, boundary handling, discretization), the relaxation / energy-minimization procedure, and a minimal set of reporting outputs (energy metrics, stability indicators, and sanity checks) so results can be compared across implementations without hidden tuning. Appendices include implementation-ready expressions and method notes aimed at reducing ambiguity and “researcher degrees of freedom.” In short: this record exists to make the broader claim testable—either others can reproduce the spectrum and ratios under stated conditions, or they can show precisely where/why it fails.